CN108588242A - A kind of SNP site of long oyster AHR genes - Google Patents
A kind of SNP site of long oyster AHR genes Download PDFInfo
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- CN108588242A CN108588242A CN201810759521.3A CN201810759521A CN108588242A CN 108588242 A CN108588242 A CN 108588242A CN 201810759521 A CN201810759521 A CN 201810759521A CN 108588242 A CN108588242 A CN 108588242A
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/124—Animal traits, i.e. production traits, including athletic performance or the like
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
Abstract
The present invention provide it is a kind of growing relevant SNP site with long oyster, the SNP site is located in Gene A HR, is sequence for SEQ ID NO:1 the 269th from the ends 5', base be C or A；The speed of growth of AA genotype individuals is significantly higher than CA genotype and CC genotype individuals.The application for the SNP marker that the present invention is had found, can substantially reduce the blindness of long oyster parental line selection, can be quickly obtained the speed of growth soon and the long oyster individual of inheritance stability is used for breeding or nursery.
Description
Technical field
The invention belongs to Biotechnology in Genetic Breeding fields, more particularly to a kind of and long relevant SNP site of oyster fast-growth.
Background technology
Long oyster (Crassostrea gigas) is also known as Pacific oyster, is to cultivate that widest in area, yield is maximum in the world
The important traditional breed variety of marine products economic shellfish and China.While the industry stable development of China head's oyster culture at present
It also begins to face many Tough questions：With frequency the problems such as cultivating intensive continuous improvement and marine environmental pollution and red tide
The breeding environment of numerous appearance, long oyster is worsening；Since nonstandard for many generations cultivation leads to inbred, long oyster is cultivated
Germplasm degradation phenomena is on the rise, and the problems such as growth is slow, dressing percentage is low, the death rate increases occurs, and seriously affects long oyster production
The sustainable development of industry；With the raising of the level of consumption and the aggravation of market competition, consumption market both domestic and external is to long oyster
Quality requirements are constantly promoted.Therefore, high-quality, high yield, degeneration-resistant improved seeds are cultivated, are that China head's oyster industry health is sustainable
The only way of development.
With the development of molecular biology and genomics, the breeding research of long oyster is also undergoing by traditional choosing
It selects, the transformation of crossbreeding to the molecular breeding based on genomic information.Molecular breeding core content based on genome is pair
The research of genotype and phenotypic polymorphism, wherein single nucleotide polymorphism (SNP) label are wide (especially in gene regions because of its distribution
Be also distributed), the advantages that high-throughput detection can be achieved, be increasingly becoming genetic marker preferred in genetic breeding research.If these
Genetic marker related to the production traits can be linked togather, you can realization carries out selection and use from DNA level, overcomes tradition side
Method is affected by human factors big unfavorable factor, improves the accuracy of selection, and may be implemented in and identify in early days with excellent
The individual of benign shape filters out excellent standby parent, so as to shorten breeding cycle, accelerates breeding process.By finding and length
The related gene of oyster fast-growth improves the screening efficiency of fast long parent, and the growth traits of predictable offspring, improves excellent
The breeding efficiency of kind.
Invention content
It marks and its applies with the relevant SNP site of long oyster fast-growth the purpose of the present invention is to provide a kind of；I.e.
One kind being located at the intragenic SNP sites of AHR.
Relevant SNP site being grown with long oyster present invention firstly provides a kind of, the SNP site is located at Gene A HR
In, be sequence be SEQ ID NO:1 the 269th from the ends 5', base be C or A；The speed of growth of AA genotype individuals is aobvious
It writes and is higher than CA genotype and CC genotype individuals.
Another aspect of the present invention provides a kind of method for detecting above-mentioned SNP site, is expanded using primer pair
The nucleic acid of detected sample, then SNP site is determined whether there is by sequencing；
The primer pair, one kind nucleotide sequence information are as follows：
Forward primer F：CAGTGGGATCTATAGTATGGGC(SEQ ID NO:2)；
Reverse primer R：CTGTTGTATTTGATTACGTGGC(SEQ ID NO:3)；
The present invention also provides a kind of kit for detecting above-mentioned SNP site, the kits, including above-mentioned draws
Object pair.
SNP site provided by the present invention is for screening long oyster breeding parent；A kind of its specific operating method is as follows：
1) measuring samples genomic DNA is extracted；
2) to extract obtained DNA as template, using specific primer to carrying out PCR amplification, PCR product is obtained；
3) pcr amplification product is sequenced, it is fast to screen to determine the genotype of the SNP marker of sample according to sequencing result
The long parent of fast-growing；The individual for the genotype that i.e. screening SNP marker is AA.
The application for the SNP marker that the present invention is had found, can substantially reduce the blindness of long oyster parental line selection, can be quick
It obtains the speed of growth soon and the long oyster individual of inheritance stability is used for breeding or nursery.
Specific implementation mode
The present invention is described in detail with reference to embodiment.
Embodiment 1：With the acquisition of the long relevant label of oyster fast-growth
1, it on the basis of completion is sequenced in long oyster genome entirely, is obtained by GWAS related analysis technologies related to growth
Gene-bHLH families.Long oyster bHLH families are classified, including A to F organizes totally 89 genes, selects on this basis
The screening that 5 candidate genes carry out SNP with the method for resurveying sequence has been selected, 417 individual wild populations are selected.Obtained 63
A site is verified in 288 individual wild populations with the method for genetic chip again, is finally carried out with biological software
Newchr17_8788640SNP labels are obtained with growth traits association analysis.The individual of Newchr17_8788640 labels, AA types
The speed of growth of individual is significantly higher than CA genotype and CC genotype individuals.
2, the association analysis of long oyster SNP site different genotype and growth traits
417 long oysters of individual wild population, measure that shell is high, shell is long, shell is wide, all weights and software weight this 5 respectively
Index, all measurement data, which meet, to be just distributed very much.Using resurveying the method for sequence to Newchr17_8788640 on AHR genes
Label analyzes that different genotype and shell are high, shell is long, shell is wide, complete with SPSS after 417 long oyster individual carries out SNP partings
Weight and software are associated analysis again.It was found that the shell of AA type individuals is high, shell is long, shell is wide, all weights and software are all higher than CA again
With CC type individuals.
3,288 long oysters of individual wild population, measure respectively shell is high, shell is long, shell is wide, all weights and software weight this 5
A index, all measurement data, which meet, to be just distributed very much.Existed to mutational site on AHR genes using the method for genetic chip
After 288 long oyster individual carries out SNP partings, with SPSS analyze different genotype and shell are high, shell is long, shell is wide, all weights and
Software is associated analysis again.It was found that the shell of AA type individuals is high, shell is long, shell is wide, all weights and software are all higher than CA and CC types again
Individual.
1 long oyster site different genotype of table in Liang Ge groups with the association analysis of growth traits
Note：Numerical value is average value scholar's standard error in table, and same row difference Superscript letters indicate significant difference (P<0.05).
Embodiment 2：Application of the SNP marker in screening the long oyster parent of fast-growth
The kit for making the assessment screening long oyster parent SNP marker of fast-growth, for detecting AHR gene SNP sites
Newchr17_8788640。
The kit contains the reagent of the specificity amplification primer and specific extension primer of required detection SNP site,
In, the specificity amplification primer sequence of site Newchr17_8788640 is SEQ ID NO:2 and SEQ ID NO:3.The reagent
Box further include common agents needed for relevant art such as, (10 × PCR (containing Mg2+) buffer solution, dNTP (10mM), distilled water, enzyme
Deng.In addition it can have standard items and control as determined gene).
Amplification reaction system includes：CDNA 1.0 μ L, 10 × PCR (containing Mg2+) buffer solution 2.5 μ L, the dNTP of concentration 10mM
2.0 μ L, the 1.0 μ L of sense primer that 10 μM of concentration, the archaeal dna polymerase 0.2 for downstream primer 1.0 μ L, concentration 5U/ the μ L that 10 μM of concentration
μ L, distilled water：17.3μL；Amplification condition：94 DEG C of 5min, 94 DEG C of 30s, 55 DEG C of 45s, 72 DEG C of 1min, totally 35 recycle, and last 72
DEG C extend 10min；Amplification PCR product is subjected to sequencing and carries out Genotyping.
SNP site is detected using kit, long oyster parent screens to fast-growth, includes the following steps：
The clip housing film edge sample from parent to be measured extracts DNA；
To extract obtained DNA as template, primary PCR amplification is carried out using specific primer, obtains first PCR product；
The PCR product obtained for the first time is sequenced, long oyster AHR bases to be measured are determined according to result after acquisition sequencing result
Whether the genotype of the SNP marker of cause is AA homozygotes to screen long oyster fast-growth individual.
Amplification reaction system includes：1.0 μ L, 10 × PCR buffer solutions of cDNA (containing Mg2+) 2.5 μ L, the dNTP of concentration 10mM
2.0 μ L, the 1.0 μ L of sense primer that 10 μM of concentration, the archaeal dna polymerase 0.2 for downstream primer 1.0 μ L, concentration 5U/ the μ L that 10 μM of concentration
μ L, distilled water：17.3μL；Amplification condition：94 DEG C of 5min, 94 DEG C of 30s, 55 DEG C of 45s, 72 DEG C of 1min, totally 35 recycle, and last 72
DEG C extend 10min；Primer is
Forward primer F：CAGTGGGATCTATAGTATGGGC(SEQ ID NO:2)；
Reverse primer R：CTGTTGTATTTGATTACGTGGC(SEQ ID NO:3)；
The results show that after the oyster parent's breeding filtered out by SNP kits to first filial generation in, find AA types
It is individual (table 2) that the shell of individual is high, shell is long, shell is wide, all weights and software are all higher than CA and CC types again, it was demonstrated that this kit is can be with
The oyster parent of quick selection and breeding merit.
Table 2：The character table of the filial generation of parent's breeding of SNP screenings
Note：Numerical value is average value scholar's standard error in table, and same row difference Superscript letters indicate significant difference (P<0.05).
Above-mentioned reaction system, reaction condition and subsequent Genotyping and appraisal procedure, can be according to known in this field normal
Know either conventional techniques to be changed or replace.The value of the kit is that the length for quickly obtaining SNP marker is male
Oyster parent improves the breeding efficiency of improved seeds to carry out molecular mark.
One embodiment of the present invention above described embodiment only expresses, the description thereof is more specific and detailed, but simultaneously
It cannot therefore be construed as limiting the scope of the patent.It should be pointed out that coming for those of ordinary skill in the art
It says, without departing from the inventive concept of the premise, various modifications and improvements can be made, these belong to the protection of the present invention
Range.
Sequence table
<110>Wanli College, Zhejiang
<120>A kind of SNP site of long oyster AHR genes
<160> 3
<170> SIPOSequenceListing 1.0
<210> 1
<211> 966
<212> DNA
<213>Artificial sequence (Artificial Sequence)
<400> 1
cattctaact tatcgacaaa atttaatttc aaaatcatat atgcatagat aagtttttca 60
tgttaataaa caatttgttg ggtgcaattt agaggcagtg ggatctatag tatgggctat 120
aaaacattca aagacgggat tggaaaaaaa ccccaaataa gccataacta attaaagaat 180
ttttatatca ttatcatttt actactatcg tttacaagta aatctgagga atttatggac 240
cacaatatca tcaacatatt gttatcagca catcaagaat atacttcgaa aactgatgca 300
atagatgaat gccacgtaat caaatacaac agtgaatcac cacagagccc aaactccttg 360
taaggtcgaa ttctgttgaa ctcaaaacac cgtatactgg gcccgtaaaa agccacggtg 420
cggatcaaat gaccccaggg acggggataa atctcggctg aaatgaggtg taacaattta 480
gaatgtttat acttgagaaa cttttaacag aaagggtttt gtcattcaac tattagatca 540
gattaagaaa tgaagctgat atcggaagac agaatagaac ttgttctcat atcaaattat 600
acgcaagata aaaaaccatc cgctgacatt ttatctacta tgacaaatac gaattctgtt 660
gggtcctatt ttggggggag agatacaaga accgccgagg caagcaaatg gcggaccacg 720
gcacagcgca aagacttgcg ttcttgtgtt tgttcattta gacggaaaat gccttataac 780
ctctttaaga agcagtagag aattcatggg aactaattat ccgcaatttt tgagggagtt 840
gcgaaaggtc aagaataaac taaaagatac cccagtatct agtttctgaa gcctatgcgc 900
caaggaagaa tgaacggcga gagcgtcaag aaaaaaactg agagaattag gggtgggaca 960
aagcct 966
<210> 2
<211> 22
<212> DNA
<213>Artificial sequence (Artificial Sequence)
<400> 2
cagtgggatc tatagtatgg gc 22
<210> 3
<211> 22
<212> DNA
<213>Artificial sequence (Artificial Sequence)
<400> 3
ctgttgtatt tgattacgtg gc 22
Claims (6)
1. a kind of growing relevant SNP site with long oyster, which is characterized in that the SNP site is located in Gene A HR, is
Sequence is SEQ ID NO:1 the 269th from the ends 5', base be C or A.
2. a kind of test right requires the method for stating SNP site described in 1, which is characterized in that the method is to use primer
SNP site is determined whether there is to expand the nucleic acid of detected sample, then by sequencing.
3. method as claimed in claim 2, which is characterized in that the sequence of the primer pair, forward primer is SEQ ID
NO:2；The sequence of reverse primer is SEQ ID NO:3.
4. a kind of primer pair for stating SNP site required for test right described in 1, which is characterized in that the primer pair,
The sequence of forward primer is SEQ ID NO:2；The sequence of reverse primer is SEQ ID NO:3.
5. the present invention also provides a kind of kit for detecting above-mentioned SNP site, the kit includes claim 4
The primer pair.
6. a kind of method for screening long oyster breeding parent, which is characterized in that the method includes following step：
1) measuring samples genomic DNA is extracted；
2) to extract obtained DNA as template, PCR amplification is carried out using the primer pair described in claim 4, obtains PCR product；
3) pcr amplification product is sequenced, the genotype of the SNP marker of sample is determined according to sequencing result to screen fast fast-growing
Long parent；The individual for the genotype that i.e. screening SNP marker is GG.
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN201810759521.3A CN108588242B (en) | 2018-07-11 | 2018-07-11 | SNP locus of crassostrea gigas AHR gene |
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| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN201810759521.3A CN108588242B (en) | 2018-07-11 | 2018-07-11 | SNP locus of crassostrea gigas AHR gene |
Publications (2)
| Publication Number | Publication Date |
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| CN108588242A true CN108588242A (en) | 2018-09-28 |
| CN108588242B CN108588242B (en) | 2021-10-01 |
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| CN201810759521.3A Active CN108588242B (en) | 2018-07-11 | 2018-07-11 | SNP locus of crassostrea gigas AHR gene |
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Cited By (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN112626238A (en) * | 2021-01-19 | 2021-04-09 | 浙江万里学院宁海海洋生物种业研究院 | Characteristic sequence for identifying crassostrea sikamea, specificity identification primer and identification method |
Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN105506162A (en) * | 2016-01-31 | 2016-04-20 | 中国海洋大学 | SNP marker related to rapid growth of pacific oysters and identification method as well as application thereof |
| CN107475413A (en) * | 2017-09-20 | 2017-12-15 | 中国科学院海洋研究所 | One kind screening improves unrighted acid C20:The related SNP of the method for the long oyster of the contents of 3 Ω 6 primer pair |
-
2018
- 2018-07-11 CN CN201810759521.3A patent/CN108588242B/en active Active
Patent Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN105506162A (en) * | 2016-01-31 | 2016-04-20 | 中国海洋大学 | SNP marker related to rapid growth of pacific oysters and identification method as well as application thereof |
| CN107475413A (en) * | 2017-09-20 | 2017-12-15 | 中国科学院海洋研究所 | One kind screening improves unrighted acid C20:The related SNP of the method for the long oyster of the contents of 3 Ω 6 primer pair |
Non-Patent Citations (2)
| Title |
|---|
| HAIGANG QI ET AL.: "Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas)", 《PLOS ONE》 * |
| 陈钰等: "长牡蛎转化生长因子受体基因多态性与生长性状和糖原含量的相关性分析", 《中国海洋大学学报》 * |
Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN112626238A (en) * | 2021-01-19 | 2021-04-09 | 浙江万里学院宁海海洋生物种业研究院 | Characteristic sequence for identifying crassostrea sikamea, specificity identification primer and identification method |
| CN112626238B (en) * | 2021-01-19 | 2022-02-22 | 浙江万里学院宁海海洋生物种业研究院 | Characteristic sequence for identifying crassostrea sikamea, specificity identification primer and identification method |
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